RetrogeneDB ID: retro_ptro_2176

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:103382072..103382725(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: EIF3K
• Ensembl ID: ENSPTRG00000010934
• Aliases: EIF3K, EIF3S12
• Description: Eukaryotic translation initiation factor 3 subunit K [Source:UniProtKB/TrEMBL;Acc:H2QG88]

Sequence

>retro_ptro_2176
ATGGTGATATTTGAGCAGATGAGAGCCAATGTGGGCATGTTGCTCCAGGGTATCAACAGGAACAATCCTGAGAAGCTGGC
CACCCTGGAGTGCTACGTGGAGATGCAGGCCAAGGACACTGCCTATGATCTGGAAGCCAACCCAGTTGTCCTGAAGCTGT
ACCAGTCCAACCCAGCGTTTTTTCAGACCACGGACACTGCCCAGATCCAGCTGAAGGCCCTCACCAACCTGCCACATACC
AACTTCACCCCGTGTAAGTGCATGATTGGCCAGGCACATCAAGAAGAGTGGCCATCTGACAGATTTTGTATCTCAAGGGC
CTGCTGGAGACCAGCCTCTTTCAGGCCTTCTGGGAAGCCCTGGATGAAAACGTGGACCTCTTGGAAGGTATAACTGGCTT
TGAAGACTCTGTCCGAATGTGTATCTGCCCTGTCGTGGGTATCACTTACCAGCACATCGACCACTGGCTGCTGGCCGAGA
TGCCTGGGTATCTGTCGGACAGCCAGCTGAAGGTGTGGATGAGAAAATAGACCTGGAGGGCTGACGAGTCCCAGCAGATC
TTCATCTGTAGCCAGGAAGAGAACATTAAGCCCAAGAACCCTGTGGAGAAGATAGACTTTGACAGTGTGTCCAGCATCAT
GGCCTTCTTCCAG

Alignment

ORF - retro_ptro_2176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMFEQMRANVGKLLKGIDRYNPENLATLERYVETQAKENAYDLEANLAVLKLYQFNPAFFQTTVTAQIL
          M..FEQMRANVG.LL.GI.R.NPE.LATLE.YVE.QAK..AYDLEAN..VLKLYQ.NPAFFQTT.TAQI.
Retrocopy MVIFEQMRANVGMLLQGINRNNPEKLATLECYVEMQAKDTAYDLEANPVVLKLYQSNPAFFQTTDTAQIQ

Parental  LKALTNLPHTDFTLCKCMIDQAHQEERP-IRQILYLGDLLETCHFQAFWQALDENMDLLEGITGFEDSVR
          LKALTNLPHT.FT.CKCMI.QAHQEE.P.I.QILYL..LLET..FQAFW.ALDEN.DLLEGITGFEDSVR
Retrocopy LKALTNLPHTNFTPCKCMIGQAHQEEWP<I*QILYLKGLLETSLFQAFWEALDENVDLLEGITGFEDSVR

Parental  KFICHVVGITYQHIDRWLLAEMLGDLSDSQLKVWMSKYGWSADESGQIFICSQEESIKPKNIVEKIDFDS
          ..IC.VVGITYQHID.WLLAEM.G.LSDSQLKVWM.K..W.ADES.QIFICSQEE.IKPKN.VEKIDFDS
Retrocopy MCICPVVGITYQHIDHWLLAEMPGYLSDSQLKVWMRK*TWRADESQQIFICSQEENIKPKNPVEKIDFDS

Parental  VSSIMASSQ
          VSSIMA..Q
Retrocopy VSSIMAFFQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.38 RPM	76.43 RPM
SRP007412_cerebellum	0.32 RPM	52.70 RPM
SRP007412_heart	0.09 RPM	40.43 RPM
SRP007412_kidney	0.18 RPM	105.10 RPM
SRP007412_liver	0.03 RPM	58.95 RPM
SRP007412_testis	0.84 RPM	30.46 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2176 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2176 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3224
Gorilla gorilla	retro_ggor_2192
Pongo abelii	retro_pabe_2673
Macaca mulatta	retro_mmul_2029
Macaca mulatta	retro_mmul_2098

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000007594	3 retrocopies	retro_etel_1653, retro_etel_1868, retro_etel_5,
Homo sapiens	ENSG00000178982	2 retrocopies	retro_hsap_2616, retro_hsap_3224,
Gorilla gorilla	ENSGGOG00000016808	1 retrocopy	retro_ggor_2192,
Myotis lucifugus	ENSMLUG00000010217	1 retrocopy	retro_mluc_645,
Macaca mulatta	ENSMMUG00000028767	2 retrocopies	retro_mmul_1478, retro_mmul_2029,
Monodelphis domestica	ENSMODG00000013314	3 retrocopies	retro_mdom_1235, retro_mdom_1929, retro_mdom_781,
Otolemur garnettii	ENSOGAG00000026260	1 retrocopy	retro_ogar_413,
Pongo abelii	ENSPPYG00000025857	4 retrocopies	retro_pabe_2342, retro_pabe_2555, retro_pabe_2610, retro_pabe_2673,
Pan troglodytes	ENSPTRG00000010934	2 retrocopies	retro_ptro_1763, retro_ptro_2176 ,
Sarcophilus harrisii	ENSSHAG00000005313	1 retrocopy	retro_shar_689,
Tarsius syrichta	ENSTSYG00000007001	1 retrocopy	retro_tsyr_1964,